Home
Publication for the ONR
grant - "Integrated Tools for Computational Chemical Dynamics"
2005 publications
"Improved
Density Functionals for Water," E. E.
Dahlke
and
D. G. Truhlar, J. Phys. Chem. A 109, 15677-15683 (2005).
"Exchange-Correlation
Functional with Broad Accuracy for Metallic and Nonmetallic Compounds,
Kinetics, and Noncovalent Interactions," Y. Zhao, N. E. Schultz, and D.
G.
Truhlar, J. Chem. Phys. 123, 161103/1-4 (2005).
"Density
Functional for
Inorganometallic and
Organometallic
Chemistry," N. E. Schultz, Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A
109,
11127-11143 (2005).
2006
publications
"Design of Density Functionals by Combining the Method of
Constraint
Satisfaction with Parametrization for Thermochemistry, Thermochemical
Kinetics,
and Noncovalent Interactions," Y. Zhao, N. E. Schultz, and D. G.
Truhlar,
J. Chem. Theory
Comput. 2, 364-382
(2006)
.
"Comparative
DFT Study of van der Waals Complexes:
Rare-Gas
Dimers, Alkaline-Earth Dimers, Zinc Dimer, and Zinc-Rare-Gas Dimers,"
Y.
Zhao and D. G. Truhlar, J. Phys. Chem. A. 110, 5121-5129 (2006)
.
"Comparative
Assessment of
DFT Methods for 3
d
Transition Metal Chemistry," Y. Zhao and D. G. Truhlar,
J. Chem. Phys. 124, 224105/1-6 (2006).
"Assessment
of Model Chemistries for Noncovalent Interactions," Y. Zhao and D. G.
Truhlar, J. Chem. Theory
Comput. 2,
1009-1018
(2006).
"Predicting
Aqueous Free Energies of Solvation as Functions of Temperature," A. C.
Chamberlin, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B, 110,
5665
(2006).
"Adding
Explicit Solvent Molecules to Continuum Solvent Calculations for the
Calculation of Aqueous Acid Dissociation Constants," C. P. Kelly, C. J.
Cramer, D. G. Truhlar, J. Phys. Chem. A 110,
2493-2499
(2006).
"Aqueous
Solvation Free Energies of Ions and Ion-Water Clusters Based on An
Accurate
Value for the Absolute Aqueous Solvation Free Energy of the Proton," C.
P.
Kelly, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B
110,
16066-16081 (2006).
"Assessment
of Density Functionals for pi Systems: Energy Differences between
Cumulenes and Poly-
ynes,
Proton
Affinities, Bond Length Alternation, and
Torsional
Potentials of Conjugated
Polyenes, and
Proton
Affinities of Conjugated Schiff Bases," Y. Zhao and D. G. Truhlar,
J. Phys. Chem. A 110, 10478-10486 (2006).
"Multi-Configuration
Molecular Mechanics Based on Combined Quantum Mechanical and Molecular
Mechanical
Calculations," H. Lin, Y. Zhao, O.
Tishchenko,
and D. G. Truhlar, J. Chem. Theory Comput. 2,
1237-1254 (2006).
"
PdnCO
(n = 1,2): Accurate Ab Initio Bond
Energies, Geometries, and Dipole Moments and the Applicability of
Density Functional
Theory for Fuel Cell Modeling," N. E. Schultz, B. F.
Gherman,
C. J. Cramer, and D. G. Truhlar , J. Phys. Chem. B 110,
24030-24036 (2006).
"A
New Local Density Functional for Main Group Thermochemistry, Transition
Metal
Bonding, Thermochemical Kinetics, and Noncovalent Interactions," Y.
Zhao,
D. G. Truhlar, J. Chem. Phys. 125, 194101/1-18
(2006).
"A
Density Functional Theory that Accounts for Medium-Range Correlation
Energies
in Organic Chemistry," Y. Zhao and D. G. Truhlar, Org. Lett. 8,
5753-5755 (2006).
"Density
Functional for Spectroscopy: No Long-Range Self-Interaction Error, Good
Performance for
Rydberg and
Charge-Transfer States,
and Better Performance on Average than
B3LYP
for
Ground States," Y. Zhao, and D. G. Truhlar, J. Phys. Chem.
A 110, 13126-13130 (2006).
"SMx Continuum
Models for Condensed Phases," C. J. Cramer and D. G. Truhlar, in
Trends
and Perspectives in Modern Computational Science, Lecture Series on
Computer and Computational Sciences, Vol. 6, edited by G.
Maroulis
and
T.E.
Simos
(Brill
Academic, Amsterdam, 2006), pp. 112-140.
2007
publications
"Transition
State Theory and Chemical
Reaction Dynamics in Solution," D. G. Truhlar and J. R. Pliego Jr., in Continuum
Solvation Models in Chemical Physics: Theory and Application,
edited by B. Mennucci and R. Cammi (Wiley, Chichester,
2007), pp. 339-366.
"Density
Functionals for Noncovalent Interaction Energies of Biological
Importance," Y. Zhao and D. G. Truhlar, J. Chem. Theory
Comp. 3, 289-300 (2007).
"Single-Ion
Solvation Free Energies and the
Normal Hydrogen
Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide",
C.P. Kelly,
C.J.
Cramer, and
D.G. Truhlar, J. Phys. Chem. B
111,
408-422 (2007).
"How
Well Can New-Generation Density Functional Methods Describe
Protonated
Epoxides Where Older Functionals Fail?" Y.
Zhao
and D. G. Truhlar, J. Org. Chem. 72, 295-298
(2007).
"Adaptive
Partitioning in Combined Quantum Mechanical and Molecular Mechanical
Calculations of Potential Energy Functions for
Multiscale
Simulations," A.
Heyden, H. Lin, and D. G.
Truhlar, J. Phys. Chem. B 111, 2231-2241 (2007).
"Computational
Electrochemistry: The Aqueous
Ru3+
|
Ru2+ Reduction
Potential," P.
Jaque,
A.V.
Marenich, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem.
C 111, 5783-5799 (2007).
"Specific Reaction
Parametrization of the AM1/d Hamiltonian
for Phosphoryl Transfer Reactions: H, O,
and P Atoms,"
K. Nam, Q. Cui, J. Gao and D. M. York, J.
Chem. Theory Comput. 3,
486-504 (2007).
"Attractive
Noncovalent Interactions in Grubbs Second-Generation
Ru
Catalysts for Olefin Metathesis," Y. Zhao and D. G. Truhlar, Org.
Lett. 9, 1967-1970 (2007).
"QM/MM: What
Have We Learned, Where are
We, and Where Do We Go from Here?" H. Lin and D. G. Truhlar,
Theor.
Chem. Acc. 117, 185-199 (2007).
"Size-Selective
Supramolecular
Chemistry in a Hydrocarbon
Nanoring," Y.
Zhao
and D. G. Truhlar, J. Am. Chem. Soc. 129,
8440-8442 (2007).
"Self-Consistent
Polarization of the
Boundary in the Redistributed Charge and Dipole Scheme for Combined
Quantum
Mechanical and Molecular Mechanical Calculations," Y. Zhang, H. Lin, D.
G.
Truhlar, J. Chem. Theory Comput. 3,
1378-1398 (2007).
"Design of a
Next Generation Force Field:
The X-
POL Potential," W.
Xie
and J.
Gao, J. Chem. Theory Comput. 3,
1890-1900 (2007).
"Self-consistent
Reaction Field Model for
Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial
Charges," A. V. Marenich, R. M. Olson, C. P. Kelly, C. J. Cramer, and
D.
G. Truhlar, J. Chem. Theory Comput. 3,
2011-2033
(2007).
"Charge Model
4 and Intramolecular Charge
Polarization," R. M. Olson, A. V. Marenich, C. J. Cramer, and D. G.
Truhlar, J. Chem. Theory Comput. 3,
2046-2054 (2007).
"Polarization
Effects in Aqueous and
Nonaqueous Solutions," A. V. Marenich, R. M. Olson, A. C. Chamberlin,
C.
J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3,
2055-2067 (2007).
"Solvatochromic Shifts of the n-->pi* Transition of Acetone from
Steam Vapor to Ambient Aqueous Solution: A Combined Configuration
Interaction QM/MM Simulation Study Incorporating Solvent Polarization,"
Y.-L. Lin, J. Gao, J. Chem. Theory Comput. 3, 1484-1493 (2007).
2008
publications
"New QM/MM Models for
Multiscale Simulation of Phosphoryl Transfer Reactions in Solution," K.
Nam, J. Gao, and D. M. York, in Miltiscale Simulation Methods for
Nanomaterials, edited by R. B. Ross and S. S. Mohanty (Wiley, 2008),
pp. 201-218.
"Benchmarking
Approximate Density Functional Theory for s/d Excitation Energies in 3d
Transition Metal Cations," N. Schultz, Y. Zhao, and
D.G.
Truhlar, J. Comp. Chem. 29,
185-189 (2008).
"Evaluation
of the
Electrostatically
Embedded Many-Body Expansion and the
Electrostatically
Embedded Many-Body Expansion of the Correlation Energy by Applications
to
Low-Lying Water
Hexamers," E. E.
Dahlke, H. R.
Leverentz,
D. G.
Truhlar, J. Chem. Theory Comput. 4, 33-41
(2008).
"A
Conservative Algorithm for an Adaptive
Change of Resolution in Mixed Atomistic/Coarse-Grained
Multiscale
Simulations," A.
Heyden and D. G. Truhlar,
J. Chem. Theory Comput. 4, 217-
221
(2008).
"Zn
Coordination Chemistry: Development
of Benchmark Suites for Geometries, Dipole Moments and Bond
Dissociation
Energies and Their Use to Test and Validate Density Functionals and
Molecular
Orbital Theory," E. A.
Amin and D. G.
Truhlar, J. Chem. Theory Comput. 4, 75-85 (2008).
"How Well Can New-Generation Density Functionals Describe the
Energetics of Bond Dissociation Reactions Producing Radicals?" Y. Zhao
and D. G. Truhlar, J. Phys. Chem. A 112,
1095-1099 (2008).
"Role of Mg
2+ in Hammerhead Ribozyme Catalysis from
Molecular Simulation," T.-S. Lee, C. S. Lopez, G. M. Giambasu, M.
Martick, W. G. Scott, and D. M. York, J. Am. Chem. Soc. 130, 3053-3064
(2008).
"Assessment
of
Multicoefficient
Correlation Methods, Second Order
Moller-Plesset
Perturbation Theory, and Density Functional Theory for
H3O+(
H2O)
n
(n=1 - 5) and OH
-(
H2O)
n
(n = 1 - 4)," E. E.
Dahlke, M. A.
Orthmeyer, and D. G.
Truhlar, J. Phys. Chem. B 112,
2372-2381 (2008).
"Extension of
a Temperature-Dependent
Aqueous Solvation Model to Compounds Containing Nitrogen, Fluorine,
Chlorine,
Bromine, and Sulfur," A. C. Chamberlin, C. J. Cramer, and D. G.
Truhlar,
J. Phys. Chem. B
112,
3024-
3039.
"The
M06 Suite of Density Functionals for
Main Group Thermochemistry, Kinetics, Noncovalent Interactions, Excited
States,
and Transition Elements: Two New Functionals and Systematic Testing of
Four M06
Functionals and Twelve Other Functionals," Y. Zhao and D. G. Truhlar,
Theor. Chem. Acc. 120, 215-241 (2008).
"Quantum Mechanical/Molecular Mechanical Simulation
Study of the Mechanism of Hairpin Ribozyme Catalysis," K. Nam, J. Gao,
and
D. M. York, J. Am. Chem. Soc. 130, 4680-4691 (2008).
"Assessment of the Accuracy of Density Functionals for
the Prediction of the Relative Energies and Geometries of Low-Lying
Isomers of
Water Hexamers," E. E. Dahlke, R. M. Olson, H. R. Leverentz, and D. G.
Truhlar, J. Phys. Chem. A 112, 3976-3984 (2008).
"Perspective
on Foundations of Solvation
Modeling: The
Electrostatic Contribution to the Free Energy of Solvation," A. V.
Marenich, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 4,
877-887 (2008).
"Computational Characterization and
Modeling of
Buckeyball Tweezers: Density Functional Study of Concave-Convex
Interaction," Y. Zhao and D. G. Truhlar, Phys. Chem. Chem. Phys. 10,
2813-2818 (2008).
"Benchmark data for interactions in zeolite
model
complexes and their use for assessment and validation of electronic
structure
methods," Y. Zhao and D. G. Truhlar, J. Phys. Chem. C 112, 6860-6868
(2008).
"A Prototype for Graphene Material
Simulation:
Structures and Interaction Potential of Coronene Dimers," Y. Zhao and
D.
G. Truhlar, J. Phys. Chem. C 112, 4061-4067 (2008).
"A Universal Approach to Solvation
Modeling," C.
J. Cramer and D. G. Truhlar, Acc. Chem. Res. 41, 760-768 (2008).
"Construction
of a Generalized Gradient
Approximation by Restoring the Density-Gradient Expansion and Enforcing
a Tight
Lieb-Oxford Bound," Y. Zhao and D. G. Truhlar, J. Chem. Phys. 128,
184109/1-8 (2008).
"Density
Functionals with Broad Applicability in Chemistry," Y. Zhao and D. G.
Truhlar, Acc. Chem. Res.
41,
157-167 (2008).
"VBSM:
A Solvation Model Based on Valence Bond
Theory," P. Su, W. Wu, C. J. Cramer, C. P. Kelly, and D. G. Truhlar,
J. Phys. Chem. A 112, 12761-12768 (2008).
"On
the
Construction of Diabatic and Adiabatic Potential Energy Surfaces," L. Song and J. Gao,
J. Phys, Chem. A 120, 12925-12935 (2008).
"Systematic
Approach for Computing Zero-Point Energy, Quantum Partition Function,
and
Tunneling Effect Based on Kleinert’s Variational Perturbation Theory,"
K.-Y.
Wong and J. Gao, J. Chem. Theory Comput., 4, 1409-1422 (2008).
"Electrostatic
Interactions in the Hairpin Ribozyme
Account for the Majority of the Rate Acceleration without Chemical
Participation
by Nucleobases," K. Nam, J. Gao, and D. M. York, RNA 14, 1501-1507
(2008).
"Comment on ‘More Accurate Generalized Gradient
Approximation for
Solids," Y. Zhao and D. G. Truhlar, Phys. Rev. B 78, 197101/1-2
(2008).
"The Variational Explicit Potential Potential and Analytical First
Derivative of Energy: Towards a Next Generation Force Field," W. Xie,
L. Song, D. G. Truhlar, and J. Gao, J. Chem. Phys. 128,
234108/1-9 (2008).
"Performance of SM8 on a Test To Predict Small-Molecule Solvation
Free Energies," A. Chamberlin, C. J. Cramer, and D. G. Truhlar, J.
Phys. Chem. B 112, 8651-8655 (2008).
"Incorporation of a QM/MM Buffer Zone in the Variational Double
Self-Consistent Field Method," W. Xie, D. G. Truhlar, and J. Gao,
J. Phys. Chem. B 112, 14124-14131 (2008).
"Improved Description of Nuclear Magnetic Resonance Chemical
Shielding Constants Using the M06-L Meta-Generalized Gradient Density
Functional," Y. Zhao and D. G. Truhlar, J. Phys. Chem. A
112, 6794-6799 (2008).
"Modeling Free Energies of Solvation in Olive Oil," A. Chamberlin,
D. Levitt, C. J. Cramer, and D. G. Truhlar, Molecular Pharmaceutics 5,
1064-1079 (2008).
"Exploring the Limit of Accuracy of the Global Hybrid Density
Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent
Interactions," Y. Zhao and D. G. Truhlar, J. Chem. Theory Comput. 4,
1849-1868 (2008).
2009
publications
"Kinetic Isotope Effects from Hybrid Classical and
Quantum Path Integral Computations," J. Gao, K.-Y. Wong, D. T. Major,
A. Cembran,
L. Song, Y.-L. Lin, Y. Fan, and S. Ma, in Kinetic Isotoped Effects in
Enzyme
Catalysis, edited by R. Alleman and M. Scruton (RSC, Biomolecular
Sciences, 2009),
pp. 105-131.
"Block-Localized Density Functional
Theory (BLDFT),
Diabatic Coupling, and Their Use in Valence Bond Theory for
Representing
Reactive Potential Energy Surfaces," A. Cembran, L. Song, Y. Mo, and J.
Gao,
J. Chem. Theory Comput., 5, 2702-2716 (2009).
"Quantum Mechanical Methods for Biomolecular
Simulations," K.-Y. Wong, L. Song, W. Xie,
D. T. Major, Y.-L. Lin, A. Cembran, and J. Gao, in Multi-scale Quantum
Models
for Biocatalysis, edited by D. M. York and T.-S. Lee (Springer, 2009),
pp.
79-101.
"On the Function of Pentameric Phospholamban: Ion
Channel or Storage Form?", L. Becucci, A. Cembran, C. B. Karim, D. D.
Thomas, R. Guidelli, J. Gao, and G. Veglia, Biophys. Journal, 96,
L60-L62
(2009).
"An Effective Hamiltonian Molecular
Orbital-Valence
Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic
Substitution Reaction of Hydrosulfide Ion and Chloromethane," L. Song,
Y.
Mo, and J. Gao, J. Chem. Theory Comp. 5, 174-185 (2009).
"Molecular Dynamics
Simulation of a Solvated Protein in Water Using an
Electronic Structure-based Explicit Polarization (X-Pol) Potential:
Polarization and Charge Redistribution in Bovine Pancreatic Trypsin
Inhibitor in Water," W. Xie, M. Orozco, D. G. Truhlar, and J. Gao,
J. Chem. Theory Comput. 5, 459-467 (2009).
"Benchmark Energetic Data in a Model System for Grubbs II
Metathesis Catalysis and Their Use for Assessment and Validation of
Electronic Structure Methods," Y. Zhao and D. G. Truhlar, J. Chem.
Theory Comput. 5, 324-333 (2009).
"Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the
Prediction of Small-Molecule Solvation Free Energies," A. Marenich, C.
J. Cramer, and D. G. Truhlar, J. Phys. Chem. B 113,
4538-4543 (2009).
"Universal Solvation Model Based on Solute Electron Density and on
a Continuum Model of the Solvent Defined by the Bulk Dielectric
Constant and Atomic Surface Tensions," A. V. Marenich, C. J. Cramer,
and D. G. Truhlar, J. Phys. Chem. B 113, 6378–6396
(2009).
"Consistent van der Waals Radii for the Whole Main Group," M.
Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and D. G. Truhlar,
J. Phys. Chem. A 113, 5806-5812 (2009).
"Thermochemical Kinetics for Multireference Systems: Addition
Reactions of Ozone," Y. Zhao, O. Tishchenko, J. R. Gour, W. Li, J. J.
Lutz, P. Piecuch, and D. G. Truhlar, J. Phys. Chem. A
113, 5786–5799 (2009).
"Non-Hermitian Multiconfiguration Molecular Mechanics," O.
Tishchenko and D. G. Truhlar, J. Chem. Theory Comput. 5, 1454-1461
(2009).
"Solvent
Dependence of 14N Nuclear Magnetic
Resonance Chemical Shielding Constants as a Test of the Accuracy of the
Computed Polarization of Solute Electron Densities by the Solvent," R.
F.
Ribeiro, A. V. Marenich, C. J. Cramer, and D. G. Truhlar, J. Chem.
Theory
Comput. 5, 2284-2300 (2009).
"Universal Solvation Model Based on the Generalized Born Approximation
with Asymmetric Descreening," A. V. Marenich, C. J. Cramer, and D. G.
Truhlar,
J. Chem. Theory Comput. 5, 2447-2464 (2009).
submitted and
in-press publications
"Efficient Approach to Reactive Molecular Dynamics
with
Accurate Forces," M. Higashi and D. G. Truhlar, J. Chem. Theory
Comput.,
available as Article ASAP (2009). DOI: 10.1021/ct900301d
"Explicit Polarization (X-Pol)
Potential Using ab
Initio Molecular Orbital Theory and Density Functional Theory," L.
Song, J.
Han, Y.-L. Lin, W. Xie, and J. Gao, J. Phys. Chem. A, available as
Article ASAP
(2009). DOI: 10.1021/jp902710a
"First principles Monte Carlo simulations of
aggregation in the superheated vapor phase of hydrogen fluoride," M. J.
McGrath,
J. N. Ghogomu, I.-F. W. Kuo, C. J.
Mundy, and J. I. Siepmann, Phys. Chem. Chem. Phys., submitted for publication,
October
2009.
"Treatment
of first-order electrostatic
interactions in saturated and superheated vapor phases," M. Dinpajooh,
N.
Rai, D. G. Truhlar, and J. I. Siepmann, Coll.
Czech. Chem. Comm., submitted for publication, October
2009 (invited
article for Ivo Nezbeda Festschrift).
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